2VG0

Rv1086 citronellyl pyrophosphate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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This is version 1.5 of the entry. See complete history


Literature

The structural basis of chain length control in Rv1086.

Wang, W.Dong, C.McNeil, M.Kaur, D.Mahapatra, S.Crick, D.C.Naismith, J.H.

(2008) J Mol Biol 381: 129-140

  • DOI: https://doi.org/10.1016/j.jmb.2008.05.060
  • Primary Citation of Related Structures:  
    2VFW, 2VG0, 2VG1, 2VG2, 2VG3, 2VG4

  • PubMed Abstract: 

    In Mycobacterium tuberculosis, two related Z-prenyl diphosphate synthases, E,Z-farnesyl diphosphate synthase (Rv1086) and decaprenyl diphosphate synthase (Rv2361c), work in series to synthesize decaprenyl phosphate (C(50)) from isopentenyl diphosphate and E-geranyl diphosphate. Decaprenyl phosphate plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan; thus, its synthesis has attracted considerable interest as a potential therapeutic target. Rv1086 is a unique prenyl diphosphate synthase in that it adds only one isoprene unit to geranyl diphosphate, generating the 15-carbon product (E,Z-farnesyl diphosphate). Rv2361c then adds a further seven isoprene units to E,Z-farnesyl diphosphate in a processive manner to generate the 50-carbon prenyl diphosphate, which is then dephosphorylated to generate a carrier for activated sugars. The molecular basis for chain-length discrimination by Rv1086 during synthesis is unknown. We also report the structure of apo Rv1086 with citronellyl diphosphate bound and with the product mimic E,E-farnesyl diphosphate bound. We report the structures of Rv2361c in the apo form, with isopentenyl diphosphate bound and with a substrate analogue, citronellyl diphosphate. The structures confirm the enzymes are very closely related. Detailed comparison reveals structural differences that account for chain-length control in Rv1086. We have tested this hypothesis and have identified a double mutant of Rv1086 that makes a range of longer lipid chains.


  • Organizational Affiliation

    Centre for Biomolecular Science, The University, St. Andrews, Scotland KY16 9RH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASE
A, B
227Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.68
UniProt
Find proteins for P9WFF5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFF5 
Go to UniProtKB:  P9WFF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFF5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.517α = 90
b = 73.541β = 90
c = 102.561γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata reduction
MOSFLMdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-13
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2018-02-07
    Changes: Database references
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Other